From 6fd7957c59215521597bb31940e92ecfdfb07ec1 Mon Sep 17 00:00:00 2001 From: Christian Mertes Date: Sun, 11 Feb 2024 20:46:22 +0100 Subject: [PATCH 1/2] cherry pick github action workflow --- .github/workflows/check-bioc.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index e32789e2..3dd4f0f7 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -52,10 +52,10 @@ jobs: fail-fast: false matrix: config: - - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } - - { os: ubuntu-latest, r: 'next', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } - - { os: macOS-latest, r: '4.2', bioc: '3.16'} - - { os: windows-latest, r: '4.2', bioc: '3.16'} + - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } + - { os: ubuntu-latest, r: 'next', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } + - { os: macOS-latest, r: '4.3', bioc: '3.18'} + - { os: windows-latest, r: '4.3', bioc: '3.18'} ## Check https://github.com/r-lib/actions/tree/master/examples ## for examples using the http-user-agent env: @@ -249,7 +249,7 @@ jobs: rcmdcheck::rcmdcheck( args = c("--no-manual", "--no-vignettes", "--timings"), build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), - error_on = "error", + error_on = "warning", check_dir = "check" ) shell: Rscript {0} @@ -313,7 +313,7 @@ jobs: if: failure() uses: actions/upload-artifact@master with: - name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results + name: ${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-results path: check ## Note that DOCKER_PASSWORD is really a token for your dockerhub From 571ee6ecefa789247b4ee36f0c605aa91e3e8edb Mon Sep 17 00:00:00 2001 From: Christian Mertes Date: Sun, 11 Feb 2024 20:52:38 +0100 Subject: [PATCH 2/2] use devel docker image for ubuntu --- .github/workflows/check-bioc.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml index 3dd4f0f7..b0a02516 100644 --- a/.github/workflows/check-bioc.yml +++ b/.github/workflows/check-bioc.yml @@ -52,8 +52,9 @@ jobs: fail-fast: false matrix: config: + # This needs to be updated after each Bioconductor release. Please make sure we have the matching R and Bioc versions in it. - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } - - { os: ubuntu-latest, r: 'next', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } + - { os: ubuntu-latest, r: 'next', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } - { os: macOS-latest, r: '4.3', bioc: '3.18'} - { os: windows-latest, r: '4.3', bioc: '3.18'} ## Check https://github.com/r-lib/actions/tree/master/examples